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Yorodumi- PDB-1fb5: LOW RESOLUTION STRUCTURE OF OVINE ORNITHINE TRANSCARBMOYLASE IN T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fb5 | ||||||
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Title | LOW RESOLUTION STRUCTURE OF OVINE ORNITHINE TRANSCARBMOYLASE IN THE UNLIGANDED STATE | ||||||
Components | ORNITHINE TRANSCARBAMOYLASE | ||||||
Keywords | TRANSFERASE / cooperativity / T-state / ornithine | ||||||
Function / homology | Function and homology information response to biotin / ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / midgut development / Urea cycle / citrulline biosynthetic process / arginine biosynthetic process via ornithine ...response to biotin / ornithine catabolic process / monoatomic anion homeostasis / ammonium homeostasis / ornithine carbamoyltransferase / ornithine carbamoyltransferase activity / midgut development / Urea cycle / citrulline biosynthetic process / arginine biosynthetic process via ornithine / Mitochondrial protein import / urea cycle / arginine biosynthetic process / amino acid binding / response to zinc ion / phosphate ion binding / liver development / response to insulin / phospholipid binding / mitochondrial inner membrane / mitochondrial matrix / response to xenobiotic stimulus / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.5 Å | ||||||
Authors | Zanotti, G. / Battistutta, R. / Panzalorto, M. / Francescato, P. / Bruno, G. / De Gregorio, A. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2003 Title: Functional and structural characterization of ovine ornithine transcarbamoylase. Authors: De Gregorio, A. / Battistutta, R. / Arena, N. / Panzalorto, M. / Francescato, P. / Valentini, G. / Bruno, G. / Zanotti, G. #1: Journal: J.Biol.Chem. / Year: 1998 Title: 1.85 A Resolution Crystal Structure of Human Ornithine Transcarbamoylase Complexed with N-phopshonacetyl-L-ornithine. Catalytic Mechanism and Correlation with Inherited Deficiency. Authors: Shi, D. / Morizono, H. / Ha, Y. / Aoyagi, M. / Tuchman, M. / Allewell, N.M. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: Substrate-induced Conformational Change in a Trimeric Ornithine Transcarbamoylase Authors: Ha, Y. / McCann, M.T. / Tuchman, M. / Allewell, N.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fb5.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fb5.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 1fb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fb5_validation.pdf.gz | 447.1 KB | Display | wwPDB validaton report |
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Full document | 1fb5_full_validation.pdf.gz | 471.6 KB | Display | |
Data in XML | 1fb5_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 1fb5_validation.cif.gz | 21.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/1fb5 ftp://data.pdbj.org/pub/pdb/validation_reports/fb/1fb5 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a trimer constructed by three identical polypeptyde chains, related by a crystallographic three-forld axis. L-norvaline is positioned in an hypothetical site, in an electron density that could represent a protein side chain. |
-Components
#1: Protein | Mass: 35888.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: LIVER References: UniProt: P00480, UniProt: P84010*PLUS, ornithine carbamoyltransferase | ||||
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#2: Chemical | ChemComp-NVA / | ||||
#3: Water | ChemComp-HOH / | ||||
Compound details | THE ACTIVE SITE CAVITY IS EMPTY AND THE PROTEIN CAN BE CONSIDEREDNonpolymer details | L-NORVALINE IS POSITIONED IN A HYPOTHETICAL SITE, IN AN ELECTRON DENSITY THAT COULD REPRESENT A ...L-NORVALINE IS POSITIONED | Sequence details | THE AUTHORS USED THE HUMAN AMINO ACID SEQUENCE, SINCE THE OVINE ONE WAS NOT AVAILABLE. ASP IS ...THE AUTHORS USED THE HUMAN AMINO ACID SEQUENCE, SINCE THE OVINE ONE WAS NOT AVAILABLE. ASP IS PRESENT AT 297 IN DATABASE REFERENCE. SHI ET AL., J.BIOL.CHEM 1998, 273:34347-24254 LISTS ALA AT 297. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 7.32 Å3/Da / Density % sol: 83.19 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 8% PEG 4000, 0.1 M Na acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298.K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.05 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→500 Å / Num. obs: 13959 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 48.7 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.3 |
Reflection shell | Resolution: 3.51→3.92 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.32 / Num. unique all: 3877 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Resolution: 3.5→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The human amino acid sequence was used, since the ovine one was not available
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Refinement step | Cycle: LAST / Resolution: 3.5→15 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor Rfree: 0.25 / Rfactor Rwork: 0.21 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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